Pure conjecture on my part but based on my experience in the airline industry and that Amtrak's reservation system seems to be based on airline reservations systems, I have a few comments.
First, regarding duplicate book detection, I very much doubt that runs instantly. Most likely an overnight process. Being duplicate booked for a few minutes is extremely unlikely to trigger anything. Given that one generally does not want to give up confirmed space until the replacement is confirmed, a short period of being duplicate booked is normal.
Regarding how the changes described above were accomplished, my guess is with a lot of overrides. Airline systems generally have a large disconnect between reservations on a plane (train) and a specific seat (room) assignment and I'd assume Amtrak is the same way. With most airlines, when you make a reservation, you first book "a" seat, then once that is confirmed reserve a "specific" seat And if the flight is overbooked or no seats are available for which you qualify for advance booking, you can be confirmed on the flight but not have a seat assignment. Given sufficient authority in the reservations system, people can have the ability to override booking limits, override fares, and just about anything else. That there is the disconnect between space on a train and specific space fits with people reporting how Amtrak will show, for instance, a bedroom available CHI-LAX on #3 but when they try to book it, they can't because it's not the same bedroom the whole distance. If right, then it is possible (again with the right supervisor/manager authority) to overbook sleeping car space.
So my guess is the Amtrak representative booked new space CHI-CIN and CIN-CVS overbooking it (reservation status would be confirmed in a bedroom but no bedroom assigned (a "no seat" as we say in the airline industry). Used override authority to force the previously held fare bucket CIN-CVS if needed. Then cancelled the original space (for those who make a distinction between canceling and modifying, this would probably be canceling the segment in the reservation being modified - almost all modifications in an airline-style reservation involve canceling something and adding something when you get down to the components of a reservation). At that point, he would be confirmed in a bedroom with no bedroom assigned, the bedroom involved would be unassigned, but there would be no salable space (for someone to steal the unassigned bedroom) because all the bedroom space was reserved. Then it's a simple matter of assigning him to the unassigned bedroom. The only risk is that someone already reserved in a bedroom calls in to change the bedroom assignment but that is a much, much smaller risk than someone without a reservation stealing the space while the changes are being made.
